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DNA methylation
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939
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Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
4.2 years ago
grayapply2009
• 0
1
vote
2
replies
1.8k
views
WGCNA on methylation data
normalization
DNA methylation
WGCNA
updated 4.9 years ago by
Peter Langfelder
★ 3.0k • written 4.9 years ago by
enora.fremy
• 0
1
vote
2
replies
975
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.5 years ago by
Lukas Chavez
▴ 570 • written 5.5 years ago by
mtefit
• 0
7
votes
7
replies
1.6k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 5.6 years ago by
Sean Davis
21k • written 5.6 years ago by
RichardJActon
▴ 50
1
vote
2
replies
1.1k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
5.8 years ago
peter.fransquet
• 0
0
votes
0
replies
754
views
iEVORA wrapping up error
differential variability
dna methylation
iEVORA
DVP
6.0 years ago
poojitha.stemcell
▴ 10
0
votes
0
replies
1.1k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
6.2 years ago
gabrielrfries
• 0
0
votes
1
reply
1.1k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
ahmad.moousavi
• 0
2
votes
5
replies
1.8k
views
Error when prepare the TCGAdata
tcgabiolinks
dna methylation
updated 6.5 years ago by
Marcel Ramos
700 • written 6.5 years ago by
michaelwxf2012
• 0
1
vote
1
reply
1.5k
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
skids121
• 0
0
votes
0
replies
1.2k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV
minfi
preprocessing
dna methylation
7.1 years ago
Thomas
• 0
1
vote
2
replies
987
views
Correlating DNA methylation and Illumina gene expression microarray data
microarray
HM450
dna methylation
cohcap
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
poojitha.stemcell
▴ 10
0
votes
1
reply
1.1k
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 7.9 years ago by
James W. MacDonald
65k • written 7.9 years ago by
fleur_p90
• 0
13 results • Page
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Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed oneā¦
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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